Catalytic nucleic acids and ligand-binding RNA and DNA aptamers have been discovered in nature and also have been derived by using in vitro evolution. As sequencing methods have become common, one theme that has emerged in biology is that proteins have recognizable domains that can be repeated, divided, or recombined in many ways. As the number of examples of nucleic acid domains grows, it has been shown that nucleic acid domains as well can be recombined in the laboratory. Interestingly, recently discovered riboswitches provide natural examples of multi-domain RNAs that exhibit this modular character.

Multi-functional nucleic acids can be engineered in the laboratory by linking together two or more separate domains in a fashion that makes them become interdependent. The junction structures can be derived either by using in vitro evolution or by modular rational design which uses rules of secondary structure to predict junction structures. In some cases, the junctions are themselves modular and can serve as general relays of conformational status between any two functional domains. These junctions are known as communication modules.